We are analyzing the mouse genome using new analytical tools and statistics to compare the results of several next generation sequencing (NGS) experiments. Data from ChIPseq, microarray and RNAseq experiments were included for analysis in order to further assess the role of HMGN1 and HMGN2 proteins in chromatin organization and gene expression. We developed analysis pipelines for ChIP-seq experiments of DNA sequences bound to HMGN1 and HMGN2 in wildtype and double knockout mice. The outcome of these collaborations is that we have developed an efficient and adjustable pipeline for the analysis of many NGS datasets in a reasonable time and can easily interrogate the data to further develop biological interpretations and devise new questions. We have analyzed epigenetic marks across the mouse genome in a variety of cell types to assess the changes that HMGN protein deficiency result in in the double knockouts, particularly in enhancer and super-enhancer regions in mouse embryonic fibroblasts, mouse embryonic stem cells, and in mouse induced pluripotent stem cells. In another collaborattion, we performed ChIP followed by massively parallel sequencing (ChIPseq) against Mediator subunits from head (Med17), middle/tail (Med14), tail (Med15 and Med2), and CDK (Cdk8) modules in budding yeast. To allow better distinction of low levels of association from experimental noise or artifacts accompanying ChIP or library amplification prior to sequencing, we compared ChIP-seq profiles from wild type yeast to med17 ts yeast after 45 min at 37C. In yeast harboring this mutation, the head module is disrupted at 37C and mRNA transcription is greatly reduced genome-wide within 30 minutes. Furthermore, comparison of ChIP against Mediator subunits and Pol II in wild type and med17 ts yeast allowed detection of decreased association of Mediator and Pol II even at constitutively active promoters having relatively low amounts of Mediator association, while the relatively short temperature shift mitigates against the likelihood of indirect effects. We also compare association of Mediator subunits and Pol II in wild type and med3 med15 yeast, which lack two of the three subunits from the tail module triad of Med2/Med3/Med15, thus providing insight into the genome-wide function of the tail module in Mediator recruitment. These experiments are currently being extended with a new set of mutants to further understand the activities of the Mediator complex in gene regulation. We show that Mediator co-activator complex regulates Ty1 retromobility by controlling the balance between Ty1i and Ty1 promoters. In other collaborations, we performed a genome-wide screen to reveal a role for the HIR histone chaperone complex to prevent mislocalization of budding yeast CENP-A. This provides insights into pathways that regulate proteolysis of Cse4 and defines a novel role for the HIR complex in preventing mislocalization of Cse4 by facilitating proteolysis of Cse4, thereby promoting genome stability. In order to better understand intron retention in RNA-seq data, we have developed a new software application, TPMCalculator, to quantify mRNA abundance of genomic features. We have applied this software to the TCGA cancer genomic data and are busy interpreting the results.